Characterization of Marine Fungal Communities Using Next Generation Sequencing Techniques
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Characterization of marine fungal communities using next generation sequencing techniques Helga Bårdsdatter Kristiansen Master Thesis Supervisors Håvard Kauserud (UiO), Marie L. Davey (UiO), Thomas Haverkamp (UiO) and Tove M. Gabrielsen (UNIS) Submitted: 01/03/14 1 Front page photo: The view over Adventfjorden and Isfjorden, looking at the sampling area for ISA station, taken at Hotellneset by the author. 2 INDEX 1. Summary _______________________________________________________________ 4 2. Introduction _____________________________________________________________5 Definition and the main groups of marine fungi ________________________________ 5 Number of marine fungi ___________________________________________________6 History ________________________________________________________________ 7 Detection and classification of marine fungi ___________________________________8 High throughput sequencing (HTS) __________________________________________8 Aim of the study ________________________________________________________ 10 3. Pelagic marine fungi in an arctic fjord ______________________________________ 11 3.1 MATERIALS AND METHODS _______________________________________________ 11 Study site and sample collection ___________________________________________ 11 DNA extraction, amplification, and sequencing _______________________________ 12 Bioinformatics _________________________________________________________ 12 Community richness and composition _______________________________________ 14 3.2 RESULTS _____________________________________________________________ 14 Data characteristics ____________________________________________________ 14 Community changes at different depths ______________________________________ 18 Community changes across season _________________________________________ 20 3.3 DISCUSSION __________________________________________________________ 26 Usage of the ITS marker in marine environments ______________________________ 26 Taxonomic diversity _____________________________________________________ 27 Community composition at different depths __________________________________ 28 Community composition across dates _______________________________________ 29 Changes in community composition ________________________________________ 30 Future perspectives _____________________________________________________ 31 4. Fungi in marine sediments detected by metagenomics pyrosequencing ___________ 32 4.1 MATERIALS AND METHODS _______________________________________________ 32 Datasets ______________________________________________________________ 32 Taxonomic classification _________________________________________________ 33 4.2 RESULTS _____________________________________________________________ 34 Data characteristics ____________________________________________________ 34 Taxonomy _____________________________________________________________ 34 4.3 DISCUSSION __________________________________________________________ 37 Taxonomy _____________________________________________________________ 38 Compositional differences between samples __________________________________ 39 Future perspectives _____________________________________________________ 40 5. Conclusion _____________________________________________________________ 41 6. Acknowledgment ________________________________________________________ 42 7. References ______________________________________________________________ 42 8. Supplementary __________________________________________________________ 50 3 1. Summary As molecular and bioinformatics techniques are used more frequently and new marine habitats are analysed, a constant increase of marine fungal diversity has been reported, suggesting that marine fungi are a diverse but somewhat ignored organism group. The overall objective of this thesis was to further increase our knowledge about fungal diversity in marine environments by (1) investigating the fungal communities in the pelagic at different depths and dates using an Illumina amplicon sequencing approach, and (2) investigating the fungal communities in sediments using a 454 shotgun metagenomic pyrosequencing dataset. From the arctic marine environment only 14.3% of the DNA amplified was of fungal origin. This demonstrated that the primer pair ITS1F-ITS2 is not fungal specific in a marine environment. In the marine sediments, fungi accounted for, on average, 13.7% of the eukaryotic reads. Yeasts dominated in the sediments samples and are probably adapted to life in anoxic marine sediments. Mortierellales (Zygomycota), which includes known marine fungi, dominated the pelagic arctic fungal communities. What may be terrestrial fungi were detected in both habitats, but it is not clear whether they were deposited and dormant in the marine environment or if they were actively growing and adapted to marine environments. The pelagic fungal communities were not structured according to location or depth, but there seemed to be a seasonal fluctuation in the pelagic communities. Lack of taxonomic coverage of fungal taxa in the reference databases proved to be one of the major obstacles in determining the fungal diversity in both studies. While my study provides insight into the fungal communities in sediments and the pelagic, it also highlights the need for improved databases and further studies with proper sampling techniques and replicates in order to determine what factors actually structures these communities and what role fungi play in the marine system. 4 2. Introduction ”Invariably when new substrata are surveyed for fungi, a wide range of new genera and species are encountered” (Jones 2011b). Fungi comprise a major component of terrestrial environments, act as degraders, parasites and symbionts (Jones 2011b; Kendrick 2000), and are ecologically important in chemical cycles and food webs (Gadd 2004). A large proportion of the total microbial diversity and biomass in terrestrial environments is fungal microbes (Lawley et al. 2004; Richards & Bass 2005). Similarly, in marine ecosystems and in the marine food web, fungi play a vital role (Jones 2011b). Even so, marine fungi are among the least studied of all marine organisms (Hyde 2002) and are understudied in comparison to their terrestrial counterparts. However there is increasing evidence showing the active role fungi play in the marine environment by participating in biogeochemical processes (Edgcomb et al., 2011). Molecular diversity estimates suggest a much more diverse range of fungi are present in marine environments than previously thought, which also points to their probable importance in particular ecological niches in the marine environment (Richards et al., 2012). Definition and the main groups of marine fungi While most organisms are defined by taxonomy, marine fungi form a group defined by physiology and ecology (Hyde & Pointing 2000). Historically marine fungi have been subdivided by taxonomy into “Filamentous fungi” and “Zoosporic fungi” (Jones & Pang 2012). Marine fungi can also be classified by their ecology as facultative or obligate. Facultative marine fungi have physiologically adapted to the marine environment and can grow and most likely sporulate in seawater, yet may originate from terrestrial and freshwater habitats. By contrast, obligate marine fungi originate from seawater and are also restricted to it, as their growth and sporulation occurs solely in seawater (Kohlmeyer & Kohlmeyer 1979). The majority of marine fungi are microscopic and represented mostly by yeast and lower zoosporic fungi (Jones & Pang 2012). Yeasts are defined by their unicellular growth form, and occur in the major fungal lineages; Basidiomycota and Ascomycota. Yeast is one of the dominant groups found in the deep sea and sediments (Bass et al. 2007; Kutty & Philip 2008). A wide range of yeast diversity is often affiliated with benthic animals in the deep sea (Nagahama et al. 2003), while sediments seem to act as a reservoir for yeast species (Singh et 5 al. 2011). Bass and colleagues (2007) showed that fungal diversity in deep-sea surficial sediments is dominated by basidiomycetes and ascomycetes; further, fungi with yeast growth forms appeared to be the dominant and most successful fungal form in the deep seas. Many new species of yeast have been described and current estimates include 1500 species in the marine environment (Fell et al. 2010). Filamentous fungi also occur in the marine habitats, but the rough environment of the ocean does not allow large, fleshy fruiting bodies to develop. Abrasion by particles, grains, waves and currents all hinder these structures growth and persistence. However fruiting bodies of smaller size fractions (2 – 4 mm) can be found. The deep sea, anchored wood and sheltered areas are some of the places such small fungal fruiting bodies have been observed. The second largest source of marine fungi isolated from the ocean are connected to algae as endophytes, epiphytes or parasites and of all known higher filamentous marine fungi one third are associated with algae, seaweeds and sea fans (Bugni & Ireland 2004; Alker et al. 2001; Zuccaro et al. 2004; Alva et al. 2002). The distribution of marine fungi seems to be limited more by temperature and oxygen deficiency (favouring yeast growth forms) than salinity (Kohlmeyer & Kohlmeyer 1979). Nevertheless, there is concern that the majority of the diversity of fungal attributes in the marine environment is overlooked (Richards et al. 2012) by focusing only on fungi able to grow in culture with distinguishing morphological